> sc_dim(sce.all.int, reduction = "tsne", mapping = aes(colour = RNA_snn_res.0.8))
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/rlang_error>
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
---
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. └─ggplot2:::print.ggplot(x)
3. ├─ggplot2::ggplot_build(x)
4. └─ggplot2:::ggplot_build.ggplot(x)
5. └─ggplot2:::by_layer(...)
6. ├─rlang::try_fetch(...)
7. │ ├─base::tryCatch(...)
8. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ └─base::withCallingHandlers(...)
12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. └─l$compute_aesthetics(d, plot)
14. └─ggplot2 (local) compute_aesthetics(..., self = self)
15. └─ggplot2:::scales_add_defaults(...)
16. └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
17. └─rlang (local) FUN(X[[i]], ...)
Run rlang::last_trace(drop = FALSE) to see 5 hidden frames.
> rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
---
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2:::print.ggplot(x)
3. │ ├─ggplot2::ggplot_build(x)
4. │ └─ggplot2:::ggplot_build.ggplot(x)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$compute_aesthetics(d, plot)
14. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
15. │ └─ggplot2:::scales_add_defaults(...)
16. │ └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
17. │ └─rlang (local) FUN(X[[i]], ...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─cli::cli_abort(...)
22. └─rlang::abort(...)
It seems that the specified column could not be found in the seurat object.
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggsc_1.0.2 patchwork_1.1.3 cowplot_1.1.1 clustree_0.5.1 ggraph_2.1.0 future_1.33.0 lubridate_1.9.3
[8] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[15] tidyverse_2.0.0 ggsci_3.0.0 harmony_1.1.0 Rcpp_1.0.11 COSG_0.9.0 R.utils_2.12.3 R.oo_1.25.0
[22] R.methodsS3_1.8.2 data.table_1.14.8 ggplot2_3.4.4 SeuratObject_4.1.3 Seurat_4.3.0 Matrix_1.6-1.1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.1 later_1.3.1 bitops_1.0-7
[5] polyclip_1.10-6 lifecycle_1.0.4 globals_0.16.2 lattice_0.22-5
[9] MASS_7.3-60 magrittr_2.0.3 plotly_4.10.3 httpuv_1.6.12
[13] sctransform_0.4.1 spam_2.10-0 sp_2.1-1 spatstat.sparse_3.0-3
[17] reticulate_1.34.0 pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5
[21] zlibbioc_1.48.0 Rtsne_0.16 GenomicRanges_1.54.1 BiocGenerics_0.48.1
[25] RCurl_1.98-1.13 yulab.utils_0.1.0 tweenr_2.0.2 GenomeInfoDbData_1.2.11
[29] IRanges_2.36.0 S4Vectors_0.40.2 ggrepel_0.9.4 irlba_2.3.5.1
[33] listenv_0.9.0 spatstat.utils_3.0-4 goftest_1.2-3 spatstat.random_3.2-1
[37] fitdistrplus_1.1-11 parallelly_1.36.0 leiden_0.4.3.1 codetools_0.2-19
[41] DelayedArray_0.28.0 ggforce_0.4.1 tidyselect_1.2.0 farver_2.1.1
[45] viridis_0.6.4 matrixStats_1.1.0 stats4_4.3.1 spatstat.explore_3.2-5
[49] jsonlite_1.8.7 ellipsis_0.3.2 tidygraph_1.2.3 progressr_0.14.0
[53] ggridges_0.5.4 survival_3.5-7 tools_4.3.1 ica_1.0-3
[57] glue_1.6.2 gridExtra_2.3 SparseArray_1.2.2 MatrixGenerics_1.14.0
[61] GenomeInfoDb_1.38.1 withr_2.5.2 fastmap_1.1.1 fansi_1.0.5
[65] digest_0.6.33 timechange_0.2.0 R6_2.5.1 mime_0.12
[69] colorspace_2.1-0 scattermore_1.2 tensor_1.5 spatstat.data_3.0-3
[73] utf8_1.2.4 generics_0.1.3 graphlayouts_1.0.2 httr_1.4.7
[77] htmlwidgets_1.6.3 S4Arrays_1.2.0 uwot_0.1.16 pkgconfig_2.0.3
[81] gtable_0.3.4 lmtest_0.9-40 SingleCellExperiment_1.24.0 XVector_0.42.0
[85] shadowtext_0.1.2 htmltools_0.5.7 dotCall64_1.1-1 scales_1.3.0
[89] Biobase_2.62.0 png_0.1-8 ggfun_0.1.3 rstudioapi_0.15.0
[93] tzdb_0.4.0 reshape2_1.4.4 nlme_3.1-164 cachem_1.0.8
[97] zoo_1.8-12 KernSmooth_2.23-22 parallel_4.3.1 miniUI_0.1.1.1
[101] pillar_1.9.0 grid_4.3.1 vctrs_0.6.4 RANN_2.6.1
[105] promises_1.2.1 tidydr_0.0.5 xtable_1.8-4 cluster_2.1.6
[109] cli_3.6.1 compiler_4.3.1 rlang_1.1.2 crayon_1.5.2
[113] future.apply_1.11.0 labeling_0.4.3 fs_1.6.3 plyr_1.8.9
[117] stringi_1.8.2 viridisLite_0.4.2 deldir_2.0-2 munsell_0.5.0
[121] lazyeval_0.2.2 spatstat.geom_3.2-7 hms_1.1.3 shiny_1.8.0
[125] SummarizedExperiment_1.32.0 ROCR_1.0-11 memoise_2.0.1 igraph_1.5.1
[129] RcppParallel_5.1.7